Commit 9c0e2819 authored by aditya.bhagwat's avatar aditya.bhagwat
Browse files

doench2016: set default chunk size to 100K

parent ad1dba07
......@@ -76,7 +76,7 @@ doench2014 <- function(
# mclapply seems like best choice: fork on linux - execute serially on win
doench2016 <- function(
contextseqs,
chunksize = 10000,
chunksize = 100000,
verbose = TRUE
){
# Assert
......@@ -95,7 +95,7 @@ doench2016 <- function(
contextchunks <- split(contextseqs, ceiling(seq_along(contextseqs)/chunksize))
cmessage('\t\tRun Doench2016 %d times on %d-seq chunks and concatenate (to preserve memory)', length(contextchunks), chunksize)
mc.cores <- if (assertive.reflection::is_windows()) 1 else parallel::detectCores()-2
unlist(mclapply(contextchunks,
unlist(parallel::mclapply(contextchunks,
function(x){
azi$predict( reticulate::np_array(x),
aa_cut = NULL,
......@@ -183,7 +183,7 @@ doench2016 <- function(
#' @export
add_efficiency <- function(
spacers, bsgenome, method= c('Doench2014', 'Doench2016')[1],
chunksize = 10000,
chunksize = 100000,
verbose = TRUE, plot = TRUE,
alpha_var = default_alpha_var(spacers)
){
......
......@@ -9,7 +9,7 @@ add_efficiency(
spacers,
bsgenome,
method = c("Doench2014", "Doench2016")[1],
chunksize = 10000,
chunksize = 1e+05,
verbose = TRUE,
plot = TRUE,
alpha_var = default_alpha_var(spacers)
......
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